Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"The effects of sulfate on the physiology, biochemistry, and intestinal transcriptome of Scylla paramamosain under low-salinity conditions","authors":"Gao Gao ,&nbsp;Yun Hu ,&nbsp;Kangxiang Qin ,&nbsp;Ziwei Fan ,&nbsp;Chunlin Wang ,&nbsp;Huan Wang","doi":"10.1016/j.cbd.2025.101502","DOIUrl":"10.1016/j.cbd.2025.101502","url":null,"abstract":"<div><div>Sulfate, a key component of seawater and sulfate-saline-alkali soil, critically impacts aquatic species' physiology. The aim of this experiment was to investigate the effects of sulfate concentration on the growth, survival, microstructure of gills and hepatopancreas, as well as the intestinal immune response and molecular mechanisms of <em>Scylla paramamosain</em>. The experimental groups were categorized as S1 (0 g/L sulfate, sulfate-free), S2 (1 g/L sulfate, optimal concentration), and S3 (2 g/L sulfate, high sulfate concentration). The results showed that with the increase of sulfate concentration in the experimental water, Survival and weight growth rates initially increased but declined at higher sulfate concentrations (<em>P</em> &lt; 0.05), while molting rates progressively decreased. The intestinal ACP and AKP levels in S2 were significantly higher than those in S1 and S3 (<em>P</em> &lt; 0.05). AST and ALT in the S2 group showed no significant difference from those in the S3 group (<em>P</em> &gt; 0.05) but were significantly lower than those in the S1 group (<em>P</em> &lt; 0.05). Sulfotransferases in the S2 group were significantly lower than those in the S1 and S3 groups (<em>P</em> &lt; 0.05). Short-term (72 h) microscopic observations of the gills and hepatopancreas revealed that the gills in both the S1 and S3 groups exhibited thickening of the gill filaments and rupture of the cuticle layer, while the hepatopancreatic tissue in the S3 group also showed enlargement of intercellular spaces, fracture of the basement membrane, and blurred boundaries. Transcriptome sequencing of the <em>S. paramamosain</em> intestine revealed significant upregulation of sulfotransferases in both S1 and S3 groups. GO annotation of DEGs indicated similar responses of <em>S. paramamosain</em> to sulfate-free and high-sulfate environments, maintaining physiological stability by activating protein processing pathways, enhancing blood-lymph coagulation, and regulating redox balance. KEGG analysis revealed that sulfate-free environments predominantly enriched lipid metabolism and secondary metabolism pathways. While those enriched in high-sulfate environments were mainly related to amino acid metabolism and secondary metabolism. The results indicate that both sulfate-free and high-sulfate concentrations affect the growth, survival, and molting rates of <em>S. paramamosain</em>, as well as inducing immune responses in the intestine. In the short term, they can cause structural changes in the gills and hepatopancreas. The intestinal transcriptome expression shows a similar response pattern, but the metabolic pathways differ. This study provides theoretical support and technical guidance for the cultivation of <em>S. paramamosain</em> under low-salinity conditions with sulfate-type saline-alkali water.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101502"},"PeriodicalIF":2.2,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143759897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The physiological and transcriptional differences between golden and brown noble scallops Chlamys nobilis","authors":"Cheng He,&nbsp;Yizhou Sun,&nbsp;Xixi Duan,&nbsp;Weili Wang,&nbsp;Chuanxu Zhang,&nbsp;Hongkuan Zhang,&nbsp;Huaiping Zheng","doi":"10.1016/j.cbd.2025.101498","DOIUrl":"10.1016/j.cbd.2025.101498","url":null,"abstract":"<div><div>Mollusks are the second Phylum in the Kingdom Animalia, which provide not only high-quality protein but also serves as a viewing function for humans due to the polymorphism in shell colors. However, the mechanisms of the differences in shell colors, especially on scallops, have rarely been studied. In this study, the shell and mantle of two different shell colors (golden and brown) of the noble scallops <em>Chlamys nobilis</em> were analyzed, including their microstructure, pigment content, and gene expression. The results showed that the golden scallop shell is golden from the outside to the inside, while the prismatic and nacreous layers in the brown scallop are lighter in color than the periostracum. Unlike the golden scallop, there was a layer of melanin vesicles at the edge of the brown scallop mantle. The total carotenoids content (TCC) in the mantle and shell of the golden scallop was significantly higher than that of the brown scallops (<em>P</em> &lt; 0.05), but the melanin content was significantly lower than that of the brown scallop (<em>P</em> &lt; 0.05). Candidate genes such as <em>BCDO1</em>, <em>CYP5A</em>, <em>CYP2J</em>, <em>CYBA</em>, <em>EP300</em>, and <em>GNAO</em> were screened from the differentially expressed genes (DEGs), and their differential expression may explain the differences in melanin and carotenoid content between the golden and brown scallops. These findings will help to understand the color polymorphism of noble scallops and provide a basis for further research on the inheritance of noble scallops.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101498"},"PeriodicalIF":2.2,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression profiling of the hemoglobin gene family under hypoxia stress in Sillago sihama","authors":"Lingwei Kong ,&nbsp;Minghui Ye ,&nbsp;Jiru Tan ,&nbsp;Wenjing Lai ,&nbsp;Jiaxin Liao ,&nbsp;Yulei Zhang ,&nbsp;Huapu Chen ,&nbsp;Yang Huang ,&nbsp;Guangli Li ,&nbsp;Changxu Tian","doi":"10.1016/j.cbd.2025.101500","DOIUrl":"10.1016/j.cbd.2025.101500","url":null,"abstract":"<div><div>Hemoglobin (Hb) plays a pivotal role in oxygen transport and is essential for the adaptive response to hypoxic stress. Studying the molecular evolution characteristics and expression pattern of <em>S. sihama</em> Hb gene family can provide theoretical basis for further revealing the roles of the <em>Hb</em> genes against hypoxia stress. This study aimed to identify the molecular evolution characteristics and expression patterns of <em>Hb</em> genes in <em>S. sihama</em>. Utilizing bioinformatics methods, we identified ten members of the <em>Hb</em> gene family within the whole genome of <em>S. sihama</em>, located on chromosomes LG16 and LG21 in a tandem repeat pattern. Phylogenetic analysis classified the Hb gene family into two subfamilies (alpha and beta), showing close relationships with the Hb gene family members of the large yellow croaker (<em>Larimichthys crocea</em>). Both phylogenetic and collinearity analysis indicated the conservation of <em>Hb</em> genes throughout evolution. The nonsynonymous substitution rate / synonymous substitution rate (<em>Ka</em>/<em>Ks</em>) results showed that its evolution was purifying selection. RNA-seq and qRT-PCR analyses revealed that five <em>Hb</em> genes were highlighted high expression levels in the heart and liver of <em>S. sihama</em>, with <em>sshba1.4</em>, <em>sshbad</em>, and <em>sshba1</em> showing significant up-regulation in response to hypoxic stress. In summary, this study highlights the vital role of the Hb gene family in the hypoxic stress response of <em>S. sihama</em>, suggesting their potential as crucial candidate genes for regulating environmental stress in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101500"},"PeriodicalIF":2.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic and proteomic analyses reveal the diverse components in the venom of a recently described spider species Macrothele washanensis","authors":"Mengmeng Zhang ,&nbsp;Wenzheng Cai ,&nbsp;Menghui Yang ,&nbsp;Mengying Zhang ,&nbsp;Luke R. Tembrock ,&nbsp;Zhibin Yang ,&nbsp;Heng Liu ,&nbsp;Zizhong Yang","doi":"10.1016/j.cbd.2025.101491","DOIUrl":"10.1016/j.cbd.2025.101491","url":null,"abstract":"<div><div>Spider venom has been shown to possess a variety of pharmacological activities with promising applications in biomedical and agricultural sciences. However, the molecular structure and functions of these toxins have only been revealed for a few species. In this study, we unveiled the venom composition of <em>Macrothele washanensis</em> venom for the first time using transcriptomics, proteomics, and bioinformatic analyses. A total of 147,492,716 Illumina valid reads were obtained from the transcriptome of the venom glands, and 3,010,024 unigenes were assembled to predict 69 putative toxin sequences, which were classified into 25 toxin superfamilies based on cysteine motifs. Crude venom proteomics analysis identified 43 toxin proteins, including 15 peptide toxins and 28 proteases, including the CAP (CRISP/Allergen/PR) protein family, acetylcholinesterase, metalloproteinases, hyaluronidase, and dermonecrotic toxin. In conclusion, the results of the present study revealed the composition of the venom of <em>M. washanensis</em>, and several peptide toxins with potential medical, such work provides the foundation for further research on the molecular functions of these venom components as well as applied studies for the use of such compounds.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101491"},"PeriodicalIF":2.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of chronic high-temperature stress on muscle tissue integrity and metabolism-related genes in Clarias fuscus","authors":"Xiaolong Li ,&nbsp;Yong Liu ,&nbsp;Cunyu Duan ,&nbsp;Lei Yang ,&nbsp;Dayan Zhou ,&nbsp;Zhixin Zhang ,&nbsp;Huapu Chen ,&nbsp;Guangli Li ,&nbsp;Chunhua Zhu ,&nbsp;Changxu Tian","doi":"10.1016/j.cbd.2025.101497","DOIUrl":"10.1016/j.cbd.2025.101497","url":null,"abstract":"<div><div>The increasing prevalence of high-temperature days due to global warming presents significant challenges for aquatic ecosystems and aquaculture practices. This study investigates the effects of chronic high-temperature stress on <em>Clarias fuscus</em>, a catfish species native to subtropical and tropical regions. The fish were cultured for 90 days under high-temperature conditions (HT, 34 °C) and normal temperature conditions (CT, 26 °C). Histological and transcriptomic analyses were conducted to assess the impact of continuous high-temperature stress on muscle tissue. Histological examination revealed significant damage in the HT group, characterized by irregular tissue arrangement, widened muscle fiber gaps, broken muscle filaments, and cracked nuclei. Transcriptomic analysis identified 975 differentially expressed genes (DEGs) in muscle tissue under high-temperature stress, with 512 genes up-regulated and 463 down-regulated. Notably, heat shock protein (Hsp) family genes, including <em>Hsp40</em>, <em>Hsp70</em> and <em>Hsp90</em>, were significantly up-regulated under heat stress. Enrichment analysis of these DEGs revealed significant alterations in protein processing, the PPAR signaling pathway, and fatty acid oxidation and metabolism within the endoplasmic reticulum. These findings suggest that <em>C. fuscus</em> experiences substantial tissue damage and a reduced metabolic response under high-temperature stress. This study provides a scientific foundation for future research on the adaptability of fish to temperature fluctuations.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101497"},"PeriodicalIF":2.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic response of male Anastrepha fraterculus (Diptera: Tephritidae) to sexual stimulation by host plant volatiles","authors":"Silvina A. Belliard ,&nbsp;Juan Hurtado ,&nbsp;Luciano M. Matzkin ,&nbsp;Santiago Revale ,&nbsp;Diego F. Segura","doi":"10.1016/j.cbd.2025.101495","DOIUrl":"10.1016/j.cbd.2025.101495","url":null,"abstract":"<div><div><em>Anastrepha fraterculus</em> is a major pest of fruits in South America. Previous studies revealed that males exposed to volatiles from guava, a likely ancestral host, intensify courtship behavior and increase mating success. However, the molecular and physiological mechanisms underlying this effect remain unknown. Here, we explore the impact of exposure to guava essential oil volatiles on the gene expression profile of adult male heads through de novo transcriptome assembly and differential expression analysis. We found 678 differentially expressed genes (FDR &lt; 0.05 and |FC| &gt; 2), 308 of which were over-expressed in exposed males and 370 in non-exposed males. The exposure treatment affected the transcription of genes putatively involved in mucus-forming, lipid metabolism and neuropeptide processing. Our findings provide the first insights into the molecular mechanisms underlying sexual stimulation in <em>A. fraterculus</em> males triggered by host fruit volatiles.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101495"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of different MT treatment methods on the ovarian transcriptome of Pampus argenteus","authors":"Ruixue Xing ,&nbsp;Zengbing Fang ,&nbsp;Yu Zhou ,&nbsp;Rui Liu ,&nbsp;Yajun Wang ,&nbsp;Danli Wang ,&nbsp;Shanliang Xu ,&nbsp;Xubo Wang ,&nbsp;Chunyang Guo","doi":"10.1016/j.cbd.2025.101496","DOIUrl":"10.1016/j.cbd.2025.101496","url":null,"abstract":"<div><div>17α-methyltestosterone (MT) is a synthetic androgen that is commonly used to induce sex reversal in teleost fish. In this study, MT treatment of <em>Pampus argenteus</em> was carried out by different methods to find the best treatment method and potential mechanism. The results showed that compared with the control group, low concentration of MT (50 mg/kg) could improve the growth performance of <em>P. argenteus</em> in 30 days. Gonadal histology showed that different treatments of MT had different inhibition on the ovarian development, and the number of oocytes decreased in the ovaries. The ovaries of the immersing treatment groups (10 μg/l) showed ovotestis state, but the male germ cells were in the spermatogonia stage. The E2 levels of the mixed feeding and immersing treatment groups was significantly higher than that of the control group (<em>P</em> &lt; 0.05). The 11-KT levels in the 100 mg/kg group was significantly higher than that in the control group (<em>P</em> &lt; 0.05). For the gonadal transcriptome analysis after MT treatment, 460, 568 and 381 DEGs were screened in the 50MT group, 100MT group and MT immersing group, respectively. The DEGs in 50 MT group were enriched in calcium signaling pathway and MAPK signaling pathway affecting gonadal development and differentiation. In 100 MT group, DEGs were mainly enriched in neuroactive ligand-receptor interaction, purine metabolism, vascular smooth muscle contraction and other pathways. The differential gene enrichment p53 signaling pathway and PPAR signaling pathway in the immersing group had an effect on the gonads. In this study, genes showing significant changes in expression after MT treatment were identified. The possible regulatory mechanism of 17α-methyltestosterone on gonadal development of <em>Pampus argenteus</em> was speculated. It provides a theoretical basis for exploring effective ways to improve the fertilization rate of <em>P. argenteus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101496"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome resequencing reveals the selection of adaptive evolution during the domestication of pearl oyster Pinctada maxima","authors":"Teng Zhang ,&nbsp;Jiawei Zhang ,&nbsp;Chuangye Yang ,&nbsp;Zhe Zheng ,&nbsp;Yongshan Liao ,&nbsp;Robert Mkuye ,&nbsp;Yongkang Hou ,&nbsp;Minxin Liang ,&nbsp;Shirong Fu ,&nbsp;Ping Wang ,&nbsp;Shijie Zhong ,&nbsp;Qingheng Wang ,&nbsp;Yuewen Deng","doi":"10.1016/j.cbd.2025.101494","DOIUrl":"10.1016/j.cbd.2025.101494","url":null,"abstract":"<div><div>The aquatic environment has a major effect on the domestication of species for aquaculture in nearshore environments. Disruptions in the ion composition of marine ecosystems have a major effect on the growth and development of aquaculture populations. However, research on the adaptation of domesticated bivalves to nearshore environments and the potential underlying regulatory mechanisms is limited. Here, we collected domesticated offspring (F₁ and F₂) and wild individuals (F₀ and P_w) of <em>Pinctada maxima</em> from nearshore areas. We performed a comprehensive genomic data analysis using whole-genome resequencing data. This comprehensive analysis facilitated the identification of signatures of selection on key genes and yielded locus information associated with critical adaptive evolutionary (AE) events during the domestication process. We also evaluated genetic diversity metrics, including observed heterozygosity (<em>H</em>_<em>o</em>), expected heterozygosity (<em>H</em>_<em>e</em>), and the Fixation index (<em>F</em>_<em>is</em>). The findings indicated that domesticated <em>P. maxima</em> may experience balancing selection. In the second-generation domesticated stock, we identified 372 candidate selection regions and 624 genes. Local AE events in the domesticated offspring populations were confirmed via quantitative polymerase chain reaction. We proposed a potential compensatory mechanism in which calcium ions for the main effector genes calmodulin (<em>PmCaM</em>) and catabolite activator protein (<em>PmCAP</em>) are cyclically cached. Our findings enhance our understanding of the mechanisms underlying the regulation of calcium ions, which is essential for the adaptation of species to variation in environmental conditions.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101494"},"PeriodicalIF":2.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of eyestalk ganglion provides new insights into the immune response of Eriocheir sinensis","authors":"Xiaoli Zhang,&nbsp;Shucheng Shao,&nbsp;Jiaxin Xu,&nbsp;Yi Zhang,&nbsp;Jinbin Zheng,&nbsp;Zhaoxia Cui","doi":"10.1016/j.cbd.2025.101492","DOIUrl":"10.1016/j.cbd.2025.101492","url":null,"abstract":"<div><div>Generally, eyestalk ganglion is regarded as a basic neuroendocrine tissue in decapods. In the past decades, increasing evidence has implied that the nervous system plays important roles in modulating the immune defense against pathogenic microorganisms. However, the molecular mechanisms of nervous system on the innate immunity of decapods remain largely unclear. In this study, we investigated the transcriptomic responses of eyestalk ganglion in <em>Eriocheir sinensis</em> challenged by <em>Vibrio parahaemolyticus</em>. A total of 77 differentially expressed genes (DEGs) were identified, and these DEGs were predicted to be involved in diverse biological pathways including thyroid hormone signaling pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway, ferroptosis, endocrine system, and neurotrophin signaling pathway. Furthermore, the results indicated that the eyestalk ganglion of <em>E. sinensis</em> could respond to the infection of <em>V. parahaemolyticus</em> by increasing the expression of antibacterial protein such as gillcin and ribosomal protein L27, meanwhile, weakening the inhibition of NF-κB pathway via down-regulating the expression of the suppressor genes such as sterile alpha and TIR motif-containing protein 1 and nicotinic acetylcholine receptor. These findings suggested that <em>V. parahaemolyticus</em> infection triggers the activation of immune response in eyestalk ganglion of <em>E. sinensis</em>, which throws lights on the crucial roles of eyestalk ganglion in crab antibacterial immunity and provides new clues and theoretical basis for disease prevention and control.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101492"},"PeriodicalIF":2.2,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143706413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genome analysis and global methylation patterns for epigenetic study in the brackish water flea Diaphanosoma celebensis","authors":"Min-Sub Kim ,&nbsp;Jin-Sol Lee ,&nbsp;Zhou Yang ,&nbsp;Atsushi Hagiwara ,&nbsp;Duck-Hyun Kim ,&nbsp;Jae-Seong Lee","doi":"10.1016/j.cbd.2025.101493","DOIUrl":"10.1016/j.cbd.2025.101493","url":null,"abstract":"<div><div>The brackish water flea <em>Diaphanosoma celebensis</em> is a crucial organism in brackish and estuarine ecosystems, acting as a key trophic link between primary producers and higher trophic levels. Its small size, short life cycle, and high reproductive capacity make it an ideal model for studying ecological responses to environmental stressors, especially in polluted environments. This study provides a chromosome-level genome assembly of <em>D. celebensis</em>, consisting of 22 chromosomes with an N50 of 4,113,329 base pairs and 95.1 % completeness, achieved by combining <em>de novo</em> assembly with Hi-C data from <em>D. dubium</em>. Whole-genome bisulfite sequencing (WGBS) revealed distinct DNA methylation patterns, with exons showing higher methylation than introns and intergenic regions. A detailed analysis identified four gene clusters based on methylation levels. Cluster δ (highly methylated), enriched for pathways related to protein processing, ribosomal activity, and ubiquitin-mediated proteolysis, suggests a regulatory mechanism for stress adaptation in <em>D. celebensis</em>. In contrast, cluster α (hypo methylated), associated with transcription regulation and neural functions, highlights genes involved in cellular processes that may respond dynamically to environmental changes. Functional gene comparisons indicated significant differences in pathways related to ion transport and ubiquitination, emphasizing the unique adaptations of <em>D. celebensis</em> to its brackish environment. These findings provide a deeper understanding of the species' genomic and epigenetic regulation, offering valuable insights for future studies on its adaptation to environmental pollutants.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101493"},"PeriodicalIF":2.2,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}